GACR 203/05/H001 Conference Prague, 2005 Book of abstracts

GACR 203/05/H001 Conference

Prague, 2005

Book of abstracts

GACR 203/05/H001

Experimental Study and ComputerModelling of Structure and Function

of Complex Molecular Systems andBio(macro)molecules

Marie Curie POLYAMPHI project

organized by Faculty of ScienceCharles University in Prague, Czech Republic

September 30, 2005, Prague

Acknowledgement

The Student conference is held in the frame of the grant project GACR203/05/H001: “Experimental Study and Computer Modelling of Struc-ture and Function of Complex Molecular Systems and Bio(macro)mole-cules”.

Financial support by the Grant Agency of the Czech Republic is grate-fully acknowledged.

Program

GACR 203/05/H001 Conference, Prague, 2005

Friday, September 30, 2005

8.30–8.40 Conference WelcomeK. Prochazka

8.40–8.55 Theoretical study of hydrogen bonded com-plexes in the ground and electronically excitedstates [L1]E. Muchova

8.55–9.10 Interaction energies of purine inhibitor – roscov-itine with cyclin-dependent kinase 2: correlatedab initio quantum chemical calculation [L2]P. Dobes

9.10–9.25 Potential Energy Surfaces of MicrosolvatedAdenine. . .Thymine, Guanine. . .Cytosine BasePair and its Methylated Analogue: MolecularDynamics/Quenching and Correlated Ab initioStudy [L3]L. Zendlova

9.25–9.40 Molecular anions at the air/water interface [L4]M. Mucha

coffee break

10.00–10.15 In Silico Structure and Mutations Studies onHuman Cystathionine β-Synthase [L5]K. Jelınek

10.15–10.30 New simulation algorithm for studying the as-sociation behavior of heteroarm star copolymer[L6]J. Havrankova

10.30–10.45 Towards CG models of polymers [L7]F. Uhlık

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10.45–11.00 Molecular dynamics simulation of time-resolvedfluorescence anisotropy decays from labeledpolyelectrolyte chains [L8]P. Kosovan

11.00–11.15 Polyelectrolyte behavior of amphiphilic micellesin aqueous solutions at low ionic strength [L9]P. Matejıcek

11.15–11.30 Clustering of Block Copolymer Micelles withPoly(2-vinylpyridine)-block-poly(ethylene ox-ide) Shells in Aqueous Solutions [L10]M. Stepanek

11.30–11.45 Polymerization of substituted acetylenes withRh complexes anchored on inorganic and or-ganic supports [L11]J. Svoboda

11.45–12.00 New Ni-based Catalytic System: Cleavage vs.Formation of C−C Bonds [L12]D. Necas

lunch break

13.30–13.45 Theoretical Study of the Nucleic Acid Interca-lating Drugs [L13]T. Kubar

13.45–14.00 Hydration and Tautomerization of Nucleic AcidBases [L14]J. Rejnek

14.00–14.15 Theoretical modeling of interaction of MUP-1protein with hydrophobic ligands vs. the exper-imental calorimetryc measurements [L15]V. Klusak

14.15–14.30 Interactions between amino acid residues in pro-teins – a computational study [L16]L. Bendova

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14.30–14.45 An Experimental and Theoretical Study of EPRHyperfine Coupling of Vanadocene(IV) Com-plexes [L17]J. Honzıcek

14.45–15.00 Brine Rejection from Freezing Salt Solutions:A Molecular Dynamics Study [L18]L. Vrbka

coffee break

15.20–15.35 Software for Description and Understanding ofElectrophoretic Processes [L19]V. Hruska

15.35–15.50 Comparative Study of Three Teicoplanin-BasedChiral Stationary Phases Using the LFERModel [L20]J. Lokajova

15.50–16.05 Investigation of mechanisms of laser fragmenta-tion of silver nanoparticles in aqueous ambient[L21]O. Damer

16.05–16.20 Laser ablation of Ag foil in aqueous medium:Effect of citrate ions [L22]K. Siskova

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6

Lectures

GACR 203/05/H001 Conference, Prague, 2005 L1

Theoretical study of hydrogen bonded complexes inthe ground and electronically excited states

Eva Muchova, Dana Nachtigallova, Pavel Hobza

Charles University, Faculty of Science, Albertov 2030, Prague 2, Czech Re-

public; e-mail: [email protected]

In the present study we are focusing on theoretical description of com-plexes containing C−H. . .O type of hydrogen bonding in the groundstate as well as on the properties of hydrogen bonded complexes inthe electronically excited states. This type of bonding occurs very fre-quently in the nature and it plays important role in stabilizing themacromolecules and mediating the interaction with solvent molecules.We studied the availability and binding capacity of the various sitesof methylphosphocholine which represents a polar head of membranelipids in order to understand structural organization of lipids. Thetheoretical investigations were supported by IR spectroscopy which iswell suited to provide information about the occurence of water binding[1,2].

We were also interested in properties of the excited states of hydro-gen bonded complexes and in processes occuring in these system afterelectronical excitation (excited state proton transfer reaction. Thesefeatures we studied in model system (HCN. . .H2O) in order to be ableto perform state-of-the-art ab initio calculations.

References

1. Pohle, W., Gauger, D. R., Bohl, M., Mrazkova, E., Hobza, P.,Biopolymers 2004, 74, 27–31.

2. Mrazkova, E., Hobza, P., Bohl, M., Gauger D. R., Pohle, W.,J. Phys. Chem. B 2005, 109, 15126–15134.

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L2 GACR 203/05/H001 Conference, Prague, 2005

Interaction energies of purine inhibitor – roscovitinewith cyclin-dependent kinase 2: correlated ab initioquantum chemical calculation

Petr Dobes, Pavel Hobza

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of

the Czech Republic and Center for Biomolecules and Complex Molecular

Systems, Prague 6, Czech Republic

Cyclin-dependent kinases 2 (cdk2) play a crucial role in regulation ofcell cycle. This enzyme catalyses the transfer of the ATP phosphate toserine and threonine residues located on a protein substrate and thusactivate other proteins. The inhibition of cdk2 plays a key role in drugdevelopment programmes addressing such different pathological con-ditions as inflammation, autoimmunity, oncology, cardiovascular neu-rodegenerative diseases. The interaction of inhibitor roscovitine with(cdk2) was investigated by correlated ab initio quantum chemical meth-ods. On the basis of these calculations we found that limited numberof amino acid residues in the catalytic cavity contributes dominantlyto the binding of roscovitine to cdk2, while other residues contributenegligible. The other finding concerns the role of the dispersion energy,which forms a dominant part of total stabilization energy.

10


Potential Energy Surfaces of Microsolvated Adeni-ne. . .Thymine, Guanine. . .Cytosine Base Pair and itsMethylated Analogue: Molecular Dynamics /Quenching and Correlated Ab initio Study

Lucie Zendlova, Martin Kabelac, Pavel Hobza

Institute of Chemistry and Biochemistry, Center for Biomolecules and Com-

plex Molecular Systems, Flemingovo n. 2., Prague 6, Czech Republic; e-mail:

[email protected]

A complete scans of the potential energy surfaces of adenine. . .thymine,guanine. . .cytosine, 9-methyladenine. . .1-methylthymine and 9-methyl-guanine. . .1-methylcytosine base pairs with one and two molecules ofwater, methanol, dimethylsulfoxide and chloroform were realized bythe molecular dynamics and molecular dynamics/quenchig technique.For the water molecules we used the Cornell et al. force field imple-mented in the AMBER7 program, for the organic solvents we usedRESP force field parameters and charges as it is recommended by Foxand Kollman. The most stable and populated structures localized werefurther fully reoptimized at the correlated ab initio level employing theResolution of Identity Moller-Plesset method with a large basis set.A systematic study of a microsolvation of these systems using a high-level ab initio approach was presented for the first time. These studiesof nucleic acids base pairs are important for finding of binding sites ofmolecules of solvent around bases and for the better understanding ofthe influence of the solvent on the stability of the structure of DNA.

References

1. Kabelac, M., Zendlova, L., Reha, D., Hobza, P., J. Phys. Chem.

B 2005, 12206-122132. Zendlova, L., Kabelac, M., Hobza, P., Chem. Phys. Chem. ac-

cepted3. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K.

M., Ferguson, D. M., Spellmeyer, D.C., Fox, T., Caldwell, J. W.,Kollman, P. A., J. Am. Chem. Soc. 1995, 117,5179-519

4. Fox, T., Kollman, P. A., J. Phys. Chem. 1998, 102, 8070-8079

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Molecular anions at the air/water interface

Martin Mucha, Babak Minofar, Pavel Jungwirth


the Czech Republic and Center for Biomolecules and Complex Molecular

Systems, Flemingovo nam. 2, Prague 6, Czech Republic

We report molecular dynamics studies on molecular ions, solvated ei-ther on water clusters or at the air/water interfaces. Ions studiedinclude SCN−, N−

3 and dicarboxylate dianions. SCN− and N−

3 ionsexhibit preference for interfacial solvation due to their large polariz-ability, in accord with recent photoelectron-spectroscopy and secondharmonic generation experiments. The solvation patterns of dicarboxy-late dianions depend on the length of their aliphatic chain. Oxalateand adipate prefer bulk solvation, whereas suberate and tetradecanoatesolvate at the interface. We attribute this result to the interplay be-tween hydrophobic and hydrophilic forces. We also demonstrate, howthe interfacial solvation facilitates the folding of the aliphatic chain.

References

1. Yang, X., Kiran B., Wang, X.-B., Wang, L.-S., Mucha, M., Jung-wirth, P., J. Phys. Chem. A 2004, 108, 7820–7826.

2. Petersen, P. B., Saykally, R. J., Mucha, M., Jungwirth, P.,J. Phys. Chem. B 2004, 109, 10915–10921.

3. Minofar, B., Mucha, M., Jungwirth, P., Yang, X., Fu, Y.-J.,Wang, X.-B., Wang, L.-S., J. Am. Chem. Soc. 2004, 126, 11691–11698.

12


In Silico Structure and Mutations Studies on Hu-man Cystathionine β-Synthase

Karel Jelınek


public

Cystathionine β-synthase (CBS) catalyzes the condensation of serineand homocysteine to form cystathionine. It is a pyridoxal 5’-phosphate(PLP) dependent enzyme having a complex domain structure. Mam-malian CBS forms homotetramers which each subunit consists of N-terminal heme containing catalytic domain and C-terminal regulatorydomain. While the role of heme in CBS is unknown, the catalysis canbe explained solely by participation of PLP in the reaction mecha-nism. CBS is further regulated by an allosteric regulator S -adenosyl-L-methionine (AdoMet).

There have been described over 100 mutations in CBS decreasing theenzyme activity by influencing the enzyme stability, binding of PLPand heme, or impair the allosteric regulation. Deficiency of CBS activ-ity leads to elevated level of potentially toxic homocysteine and causesan inherited metabolic disease homocystinuria which is characterizedby dislocated eye lenses, skeletal problems, vascular disease and mentalretardation.

The X-ray structure of truncated wild type CBS (without the C-terminus regulatory domain) with bound PLP and heme were solvedbut solving the structure of full-length enzyme is a difficult task becauseits strong tendency to aggregate and solving mutants structures is avery time consuming task. However, for understanding the influence ofmutations on enzyme activity, the knowledge of mutants structures isimportant. In this study we theoretically solved the structure of full-length enzyme by comparative protein modeling where as a templatefor the regulatory domain (called CBS domain) the X-ray structureof hypothetical protein containing CBS domain from Bacillus Subtiliswere used. Further the structure of important mutants were simulatedand several important structural characteristics were calculated. Thetheoretical results will be completed by biochemical data (measuredat the Institute of Inherited Metabolic Disorders of the First Faculty

13


of Medicine) and together will produce a basic guideline for mutationscharacterization and possibly for treatment.

14


New simulation algorithm for studying the associa-tion behavior of heteroarm star copolymer

Jitka Havrankova,


public

A new computational algorithm for dynamic lattice Monte Carlo simu-lations of the associative behavior of heteroarm copolymers in selectivesolvents was developed and optimized for efficient and relatively fastsimulation studies. The algorithm is based on the dynamic configu-ration bias Monte Carlo variant of the self-avoiding walk procedure.Simultaneously, a new criterion for recognition of an associate is pro-posed. Results on the micellization behavior of heteroarm star (mik-toarm star) copolymers are presented.

15


Towards CG models of polymers

Filip Uhlık


public

Molecular dynamics (MD) typically solves classical equations of motionfor empirical potential fitted to reproduce experimental or calculatedquantities (thermochemistry, bond lengths, . . . ). Limits of conven-tional atomistic MD are about 105 atoms for 100 ns trajectory. Formany properties of polymers this is not long enough! After reductionto 102 particles it could be 100 µs or longer. MD calculates morethan we really need. As we don’t have the massively parallel resourcesmother Nature has, we must spare. A way how to spare is to developcoarse-grained (CG) models with only interesting degrees of freedomand to use generalized Langevin equation (GLE) to calculate the trajectories. Our attempts to do this for polymers and our preliminaryresults will be described in this presentation.

16


Molecular dynamics simulation of time-resolved flu-orescence anisotropy decays from labeled polyelec-trolyte chains

Peter Kosovan


public

We present molecular dynamics simulations of time-resolved fluores-cence anisotropy decays from labeled polyelectrolyte chains. Time-resolved fluorescence measurements are often used in experiment tomonitor segmental dynamics and conformational changes of the poly-mer, however, the experiments are indirect and require additional in-formation for reliable interpretation. In a parametric study we ex-plore the effect of the solvent quality and polymer dissociation on boththe conformational behaviour and the observable time-resolved fluores-cence anisotropy decays. The simulations show a clear relation betweenthem and thus provide a basis for unambiguous interpretation of ex-perimental data. This is illustrated by comparing the simulation datato experimental data on poly(methacrylic acid).

17


Polyelectrolyte Behavior of Amphiphilic Micelles inAqueous Solutions at Low Ionic Strength

Pavel Matejıcek 1, Filip Uhlık 1, Jana Humpolıckova 1,2, Mi-lena Spırkova 3, Karel Prochazka 1

1 Charles University, Faculty of Science, Albertov 2030, Prague 2, Czech

Republic

2 The Heyrovsky Institute of Physical Chemistry of the Academy of Sciences

of the Czech Republic, Dolejskova 5, Prague 8, Czech Republic

3 Institute of Macromolecular Chemistry, Academy of Sciences of the Czech

Republic, Heyrovsky Square 2, Prague 2, Czech Republic

Amphiphilic diblock copolymer polystyrene-block -poly(methacrylicacid), PS-PMA, forms multimolecular micelles in a selective solvent.Fairly monodisperse spherical micelles were prepared by stepwise dial-ysis from water/1,4-dioxane mixtures into very pure water or aqueoussalt solutions. The micelles consist of the kinetically frozen PS coresurrounded by the micellar shell formed by PMA chains. The poly-electrolyte behavior of these micelles has been studied in detail bycombination of light scattering, fluorescence correlation spectroscopyand atomic force microscopy. Experimental results were compared andalso interpreted with the help of computer simulations. All data sug-gest that the PMA shell of kinetically frozen micelles remind moreclosely the Pincus brush than osmotic brush in a solution with a lowionic strength.

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Clustering of Block Copolymer Micelles with Poly(2-vinylpyridine)-block-poly(ethylene oxide) Shells inAqueous Solutions

Miroslav Stepanek, Pavel Matejıcek, Jana Humpolıckova, Ka-rel Prochazka


public

The key factor determining the solution behavior of poly(ethylene ox-ide) (PEO) is the presence of both hydrophobic group (−CH2CH2−)and hydrophilic, hydrogen-bonding group (−O−) in its monomer unit.This amphiphilic character of PEO manifests itself in clustering ofthis polymer in various solvents. Although there have been proposedseveral aggregation mechanisms, such as crystallization, interchain hy-drogen bonding or subtle phase separation, the exact origin of PEOclustering still remains uncertain and may be different for differentexperimental conditions including solvent, concentration and temper-ature.

In this communication, we report on clustering of block copolymermicelles with PEO shells in aqueous solutions. Clusters of polystyrene-block -poly(2-vinylpyridine)-block -poly(ethylene oxide) (PS-PVP-PEO)micelles were studied and characterized both in solution and on micasurface by static and dynamic light scattering, fluorescence correlationspectroscopy and atomic force microscopy.

Obtained results show that aggregation of PS-PVP-PEO micelles isboth concentration- and pH-dependent. Cluster formation in acidaqueous solutions is hindered by repulsive electrostatic interaction be-tween inner shells of protonated poly(2-vinylpyridine). Clusters foundon mica surface by atomic force microscopy imaging have a relativelyloose structure in which individual micelles can be resolved.

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Polymerization of substituted acetylenes with Rhcomplexes anchored on inorganic and organic sup-ports

Jan Svoboda 1, Hynek Balcar 2, Jan Sedlacek 1, Jirı Vohlıdal 1

1 Charles University, Faculty of Science, Albertov 2030, Prague 2, Czech

Republic; e-mail: [email protected]

2 The Heyrovsky Institute of Physical Chemistry of the Academy of Sciences

of the Czech Republic, Dolejskova 5, Prague 8, Czech Republic

Complexes [Rh(COD)OCH3]2, [Rh(COD)Cl]2 and [Rh(NBD)Cl]2(COD = cycloocta-1,5-diene, NBD = norbornadiene) which are knownas efficient homogenous catalysts of substituted acetylenes polymeriza-tion were anchored on (i) siliceous mesoporous molecular sieves of theMCM-41, MCM-48 and SBA-15 type either directly ([Rh(cod)OCH3]2)or via (NH2(CH2)3Si(OCH3)3 or PPh2(CH2)2Si(OC2H5)3 spacer (Cl-bridged complexes) and (ii) commercially available polybenzimidazole(direct anchoring of Cl-bridged complexes).

Heterogeneous catalysts with COD-containing Rh complexes anchoredeither directly or via N-containing linker were found highly activein polymerization of phenylacetylene (PhA) and its ring-substitutedderivatives into cis-transoid poly(PhA)s the molecular weight of which(Mw = 1 · 105 – 4 · 105) was higher as compared to that achieved withhomogeneous [Rh(COD)OCH3]2 and [Rh(COD)Cl]2 catalysts. Hetero-geneous catalysts with NBD-containing Rh complex and catalysts inwhich P-containing linker was applied (for anchoring both NBD- andCOD- containing complexes) were either non-active or exhibited onlymarginal activity in PhA polymerization.

The catalytic activity of all above discussed catalysts was found to besteadily bound to the solid phase, catalysts were found to be resistantto metal leaching and were easily separated from the reaction products.Polymers prepared with these catalysts are free of catalyst residua andare suitable for special applications.

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New Ni-based Catalytic System: Cleavage vs. For-mation of C−C Bonds

David Necas, Matyas Tursky, Martin Kotora



The C−C bond activation (cleavage) as well as the C−C bond forma-tion under mild and simple reaction conditions are intensively soughtafter processes.[1] Recently, we have developed a simple and useful cat-alytic system based on nickel phosphine complexes that can be used forthe smooth C−C bond cleavage reaction in various allylmalonates.[2]Herein we would like to present that just a slight change of the reactionconditions can selectively alter the course of the reaction to the C−Cbond forming reaction. For example, the reaction of 1,6-heptadienes(malonic ester derivatives) can result either in C−C bond cleavage(deallylation) or C−C bond formation (cyclization).

The deallylation is catalyzed not only with Ni-complexes but also byother transition metal complexes with various level of selectivity. TheNi-catalyzed cyclization is quite general with respect to variously sub-stituted 1,7-dienes. The scope, generality and synthetic application ofthe both reactions will be discussed.

This work has been supported by Project No. 1M6138896301 to theCentre for New Antivirals and Antineoplastics from Ministry of Edu-cation of the Czech Republic and by the Grant Agency of the CzechRepublic (grant No. 203/03/H140).

References

1. Activation of Unreactive Bonds and Organic Synthesis, Top.Organomet. Chem., 3, 1999, 1-192

2. Necas D., Tursky M., Kotora M., J. Am. Chem. Soc., 126, 2004,10222

21


Theoretical Study of the Nucleic Acid IntercalatingDrugs

Tomas Kubar, Pavel Hobza

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sci-

ences, Flemingovo nam. 2, Praha 6, Czech Republic;

e-mail: [email protected], [email protected]

The aim of the anti-tumor chemotherapy is to stop the DNA replica-tion and/or transcription process. The group of effective substancesincludes small organic molecules containing a polycyclic aromatic part,which bind to the DNA by the intercalative mode, i.e. they insert inbetween two successive base pairs of the DNA. However toxic, thesecompounds have been clinically applied with success.

We have explored various characteristics of the binding of a model in-tercalator ethidium to DNA using the methods of computational chem-istry. Although the process of intercalation was thoroughly studied ex-perimentally, the computational approach is suited better to describeits intrinsic nature and energy relationships.

The electronic structure of ethidium and its derivatives was studiedand the amount of electron transfer in the complex with DNA wasevaluated. A method for calculation of the interaction energy was pro-posed and applied to the drug. . . DNA complex; moreover, the methodis worth recommendation for further intercalator evaluation and de-sign. The demands on the structure of a potent intercalator wereconfirmed and explained. The magnitude of the free energy of inter-calation and its components was estimated. The methodology for thebinding free energy difference calculations was designed, which shouldbecome a useful tool in the rational drug design.

References

1. Kubar, T., Hanus, M., Ryjacek, F., Hobza, P., Chem. Eur. J.

2005, in press.

22


Hydration and Tautomerization of Nucleic Acid Ba-ses

Jaroslav Rejnek, Pavel Hobza


the Czech Republic, Na Santince 5, Prague 6, Czech Republic;

e-mail: [email protected]

Nucleic acid bases are dominantly present in the most stable canonicalform, but their rare tautomers may be involved in various biologicalprocesses including point mutations. Their presence in biomolecules isnevertheless rather rare. The situation is different in gas-phase exper-iments where various tautomers coexist. Although gas-phase is veryfar from native environment, the first more native insight is passingfrom the gas-phase to bulk water. Water can dramatically change therelative stability of various tautomers, which requires a description ofhydration effects. Different tautomers of guanine, adenine, thymineand uracil were studied in the gas phase, in a microhydrated environ-ment and in bulk water environment using the molecular dynamics-thermodynamic integration method (MD-TI), conductor-like polariz-able continuum model (C-PCM, COSMO) and a hybrid model (C-PCM + explicit water molecules).

23


Theoretical modeling of interaction of MUP-1 pro-tein with hydrophobic ligands vs. the experimentalcalorimetryc measurements

Vojtech Klusak, Lubomır Rulısek, Jirı Vondrasek, Pavel Hob-za

Institute of organic chemistry and biochemistry, Czech Academy of Science,

Flemingovo nam. 2, Prague 6, Czech Republic; e-mail: [email protected],

[email protected]

We are optimizing a theoretical description suitable for modeling ofthe interaction of nonpolar (hydrophobic) ligands with proteins. Themodel system, MUP-1 protein, has several advantages for our purpose.It is binding hydrophobic ligands that are rather small. There arecalorimetric measurements available for whole set of complexes of theprotein and its mutants and for most of them the X-ray structures arealso available.

The important point in modeling of the nonpolar, hydrophobic systemsis the correct description of the enthalpic term. [1, 2] As was shownby calorimetric measurements, this is exactly the case for our system.[3, 4] The methods that are used include quantum mechanics, classicalmechanics, continuum and explicit models of solvent.

References

1. Klusak, V., Havlas, Z., Rulısek, L., Vondrasek, J., Svatos, A.,Chem. Biol. 2003, 10, 331–340.

2. Vondrasek, J., Bendova, L., Klusak, V., Hobza, P., J. Am. Chem.

Soc. 2005, 127, 2615–2619.3. Bingham, R.J., et. al., J. Am. Chem. Soc. 2004, 126, 1675–1681.4. Sharrow, S. D., et. al., Biochemistry 2003, 42, 6302–6309.

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Interactions between amino acid residues in proteins– a computational study

Jirı Vondrasek, Lada Bendova, Vojtech Klusak, Pavel Hobza


the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic

We present a high-level ab initio computational study (MP2/completebasis set limit + CCSD(T) correction term)[1, 2] of the interactions be-tween amino acid residues inside hydrophobic core of a protein. In ourmodel system – protein rubredoxin, the stabilization energy amountedto ∼ 50 kcal/mol, which demonstrates that the hydrophobic core isstabilized by strong attractive forces. This is incontradiction to thecurrent opinion that the formation of a hydrophobic core of globularprotein is an example of a classical hydrophobic effect [3] characterizedby small contribution of complexation enthalpy. We also show that theDFT methods are unsuitable for the description of interactions withprevailing dispersion character. Our findings are of great importancefor the molecular dynamics simulations of proteins and furthermoremay lead to substantial changes inthe current view of protein folding[4].

References

1. Halkier, A., Helgaker, T., Jurgensen, P., Klopper, W., Koch, H.,Olsen, J.; Wilson, A. K., Chem. Phys. Lett. 1998, 286, 243

2. Jurecka, P.; Hobza, P., Chem. Phys. Lett. 2002, 365, 893. Meyer, E. A., Castellano, R. K., Diederich, F., Angew. Chem.,

Int. Ed. 2003, 42, 12104. Vondracek J., Bendova L., Klusak V., Hobza P., J. Am. Chem.

Soc. 2005, 127 (8), 2615-2619

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An Experimental and Theoretical Study of EPR Hy-perfine Coupling of Vanadocene(IV) Complexes

Jan Honzıcek 1,2, Jaromır Vinklarek 1, Petr Nachtigall 1,2

1 Department of General and Inorganic Chemistry, University of Pardubice,

nam. Cs. legiı 565, Pardubice, Czech Republic

2 Institute of Organic Chemistry and Biochemistry, Academy of Sciences of

the Czech Republic and Center for Complex Molecular Systems and Biomole-

cules, Flemingovo namestı 2, Prague, Czech Republic

Vanadocene(IV) complexes of Cp2VX2 (X = halide, pseudohalide) arecurrently investigated due to their biological activity [1]. The EPRspectroscopy is the method suitable for experimental study of thesesystems. Vanadocene(IV) complexes show a strong hyperfine split-ting (Aiso = 170–220 MHz) due to the interaction of unpaired elec-tron with the 51V nucleus (I=7/2; 99.8 %). One of the problems ofEPR experiments is the assignment of experimental EPR parametersto a particular complex structure when the structure is not known fromanother experimental technique. Recently, hyperfine coupling of somevanadium(IV) compounds was theoretical studied on density functionallevel of theory (DFT) [2,3].

We prepared a series of new vanadocene complexes and confront theobserved values of Aiso constants with these calculated using variousexchange-correlation functionals. It was found that Aiso calculatedwith B3PW91 functional correlates well with experimental Aiso forbroad range of vanadocene compounds. Simple scaling of calculatedAiso was proposed. Scaled isotropic constants are in very good agree-ment with experimental parameters. It is shown that structure ofvanadocene complex can be assigned based on the comparison of ex-perimental and theoretical HFC tensors.

References

1. Navara, C. S.; Benyumov, et al., Anti-Cancer Drugs 2001, 12,369

2. Munzarova, M. L.; Kaupp, M., J. Phys. Chem. B 2001, 105,12644

3. Saladino, A. C.; Larsen, S. C., J. Phys. Chem. A 2003, 107,1872

26


Brine Rejection from Freezing Salt Solutions:A Molecular Dynamics Study

Lubos Vrbka, Pavel Jungwirth

Center for Biomolecules and Complex Molecular Systems and Institute of

Organic Chemistry and Biochemistry, Academy of Sciences of the Czech

Republic, Prague; [email protected]

Liquid water is an excellent solvent which is capable of dissolving mo-lar amounts of common inorganic salts such as NaCl. On the otherhand, salts are almost insoluble in ice, with solubilities in the micro-molar range at best. This fact is behind a very interesting natural phe-nomenon ?- brine rejection from freezing aqueous salt solutions – thathas several important consequences both in nature (water masses cir-culation, thundercloud electrification) and technology (desalination).

Despite its general importance, the microscopic mechanism of this pro-cess is still missing. Here molecular dynamics can serve as an ideal toolfor gaining more insight into the problem.

After brief introduction recent results of our molecular dynamics sim-ulations of water freezing and brine rejection will be briefly presented.Proposed mechanism of salt rejection from freezing solution will bealso discussed.

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Software for Description and Understanding of Elec-trophoretic Processes

Vlastimil Hruska, Michal Jaros, Bohuslav Gas



We are engaged in theoretical description of electrophoretic processes,development of electrophoretic software, and experimental validationof our theoretical conclusions. The description of the electrophoreticsystem is based on a set of partial differential equations respectingmass conservation, dissociation equilibria of weak acids, bases or am-pholytes, autoprotolysis of solvent, and electroneutrality.

We created computer programs PeakMaster and Simul (available onour web pages [1]), which process the set of partial differential equa-tions in different ways. Program PeakMaster solves linearized equa-tions [2, 3] and its outputs are the velocities and detection responsesof all zones in the system, pH and conductivity of background elec-trolyte. PeakMaster is a tool for fast-finding background electrolytecompositions to achieve the best performance of experimental analyses(dry-lab optimalization). The Simul program solves the set of equa-tions numerically thus it gives exact solution of the model defined byinitial conditions. Simul provides detailed information about the elec-trophoretic system; however, its demands for computation time andfor user skills are higher than in program PeakMaster.

References

1. http://www.natur.cuni.cz/gas

2. Stedry M., Jaros M., Hruska V., Gas B., Electrophoresis 2004,25, 3071-3079

3. Jaros M., Hruska V., Stedry M., Zuskova I., Gas B., Electrophore-

sis 2004, 25, 3080-3085

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Comparative Study of Three Teicoplanin-Based Chi-ral Stationary Phases Using the LFER Model

Jana Lokajova, Kveta Kalıkova, Eva Tesarova,



Teicoplanin is a macrocyclic antibiotic that is highly effective as a chiralselector for enantiomeric separations. In this study, we used threeteicoplanin based chiral stationary phases (CSPs) native teicoplanin,teicoplanin aglycone and recently synthetized methylated teicoplaninaglycon.

The similarities and differences in retention characteristics of comparedCSPs have been characterized by the use of linear free energy relation-ships (LFER). Capacity factor, ki, determined for a set of solutes ofstructurally different compounds on compared columns have been usedto calculate the regression coefficients of the LFER equations. The re-gression coefficients obtained reveal the different types of molecularinteractions and their contribution to retention processes of the char-acterized stationary phases. Since the same mobile phase was usedwith the different columns, the regression coefficients characterize justthe various chiral stationary phases. The mobile phases applied showedinteresting results in chiral separations of some structurally differentcompounds on the investigated CSPs. These results have been relatedwith the LFER evaluation.

The results show the complexity of the interaction forces participatingin the retention. The considerable contribution towards the retentionis intermolecular interaction of hydrophobic type on all these CSPs inthe mobile phase with high aqueous portion [1]. The difference in hy-drogen bond acidity between the stationary and mobile phases and theinteractions with n- and π-electrons also contribute to the interactionmechanism on the T and MTAG CSPs. However, the proportions ofthe respective coefficients to the other ones considerably decrease withincreasing organic modifier concentration in the mobile phase. Thecontributions of all the individual molecular interactions are gettingsignificant and the separation systems of all the compared CSPs seemto become more similar. The relative contribution of the individual

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molecular interactions clearly changes with both the teicoplanin struc-ture variation and mobile phase composition.

References

1. Lokajova J., Tesarova E., Armstrong D. W., J. Chromatogr. A

2005, 1088, 57–66.

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Investigation of mechanisms of laser fragmentationof silver nanoparticles in aqueous ambient

Ondrej Dammer, Jirı Pfleger, Blanka Vlckova, Karolına Sis-kova, Miroslav Slouf


public

Institute of Macromolecular Chemistry, Academy of Sciences of the Czech

Republic, Heyrovsky Sq. 2,Prague 6, Czech Republic;

e-mail: [email protected]

We report on the investigation of interaction of a high energy pulsedlaser irradiation with a highly polydisperse hydrosol containing Agnanoparticles. The study is focused on the process of nanoparticlesfragmentation with respect to their shapes and sizes, and to the wave-length and energy of the NdYAG laser pulses used for the fragmen-tation. We performed a set of in?situ optical absorption studies thatallowed us to observe the changes in the fragmented hydrosol after eachof the subsequent pulses as well as ex?situ TEM studies of the nanopar-ticles at the selected stages of the fragmentation process. A good agree-ment was observed between the experimentally found morphology ofsilver nanoparticles in hydrosols after the fragmentation by laser pulsesat various wavelengths and the theoretical predictions.

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Laser ablation of Ag foil in aqueous medium: Effectof citrate ions

Karolına Siskova 1,2,3, Blanka Vlckova 1,2,3, Jirina Hromadko-va 4, Miroslav Slouf 4

1 Charles University in Prague, Hlavova 2030, 128 40 Prague, Czech Repub-

lic; e-mail: [email protected]

2 Pierre-Yves Turpin, BioMoCeTi – Universite P. et M. Currie Paris VI,

GENOPOLE Campus 1, Evry, France

3 Claire Fayet, Service de Microscopie Electronique de l´IFR M 83 de Bi-

ologie Integrative – CNRS – Paris VI, France

4 Ustav makromolekularnı chemie AV CR, Heyrovskeho namestı 2, Praha,

Czech Republic

Promoting effect of citrate in 1·10−5 – 1·10−2M concentrations on laserablation (LA) of a Ag foil in aqueous solution performed by ns laserpulses at 1064 nm is reported. Furthermore, adsorption of citrate ionswas found to increase markedly the stability of the resulting LA-Ag hy-drosol. The results are discussed on the basis of comparison of surfaceplasmon extinction spectral characteristics, transmission electron mi-croscopy images, nanoparticle size distributions and surface-enhancedRaman scattering (SERS) spectral tests of hydrosols resulting from LAin neutral and acidic aqueous citrate solutions and in pure water.

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Posters

GACR 203/05/H001 Conference, Prague, 2005 P1

Probing strong optical fields in compact aggregatesof silver nanoparticles by SERRS of protoporphyrinIX

Magdalena Sladkova 1, Blanka Vlckova 1, Peter Mojzes 2, Mi-roslav Slouf 3, Coralie Naudin 4, Gwenelle Le Bourdon 4

1 Department of Physical and Macromolecular Chemistry, Charles University

in Prague, Hlavova 2030, Prague 2, Czech Republic

2 Institute of Physics, Charles University in Prague, Ke Karlovu 5, Prague 2,

Czech Republic

3 Institute of Macromolecular Chemistry Academy of Sciences of Czech Re-

public, Heyrovsky Sq. 2, Prague 6, Czech Republic

4 Jobin-Yvon S.A.S., 231, rue de Lille, 59650 Villeneuve d’Ascq, France

TEM images and measurements of SERRS (surface-enhanced reso-nance Raman scattering) spectra as a function of the porphyrin concen-trations in systems with unmodified and chloride-modified Ag nanopar-ticles and protoporphyrin IX (PPIX) are reported. TEM images haveshown formation of compact aggregates in systems with chloride mod-ified Ag nanoparticles, as opposed to systems with the unmodifiedparticles constituted by isolated particles. SERRS spectra of PPIXas a function of PPIX concentration were measured and subjected tofactor analysis. Two spectral components were identified and ten-tatively attributed to unperturbed PPIX and to Ag+-PPIX surfacespecies. Concentration value of the SERRS spectral detection limit ofthe latter species was determined to be nearly three orders of magni-tude lower in system with the compact aggregates than in the systemwith separated nanoparticles and achieves the value of 1 · 10−10 M ina macrosampling Raman experiment. TEM images and SERRS-micro-Raman spectra of single compact aggregates of chloride-modified Agnanoparticles incorporating PPIX molecules were acquired from a sam-ple prepared by attachment of the aggregates to amine groups of deriva-tized, SiOx/formvar coated copper grids for TEM. The SERRS signalhas shown large temporal fluctuations as well as variations from oneaggregate to another. Within the signal fluctuations, a SERRS spec-trum showing the characteristic bands of both SERRS spectral formsof PPIX and originating most probably from a few PPIX molecules

35

P1 GACR 203/05/H001 Conference, Prague, 2005

located in hot spots in the interstices between the Ag nanoparticles,was obtained.

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Authors

Bendova, Lada, 25

Dammer, Ondrej, 31Dobes, Petr, 10

Havrankova, Jitka, 15Honzıcek, Jan, 26Hruska, Vlastimil, 28

Jelınek, Karel, 13

Klusak, Vojtech, 24, 25Kosovan, Peter, 17Kubar, Tomas, 22

Lokajova, Jana, 29

Matejıcek, Pavel, 18, 19Mucha, Martin, 12Muchova, Eva, 9

Necas, David, 21

Rejnek, Jaroslav, 23

Sladkova, Magdalena, 35Svoboda, Jan, 20

Siskova, Karolına, 31, 32Stepanek, Miroslav, 19

Uhlık, Filip, 16, 18

Vrbka, Lubos, 27

Zendlova, Lucie, 11

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GACR 203/05/H001 Conference Prague, 2005 Book of abstracts

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